The story centers around three characters—Uesugi Kazuya, his twin older brother Tatsuya, and Asakura Minami. Kazuya is the darling of his town as he's talented, hardworking, and the ace pitcher for his middle school baseball team. Tatsuya is a hopeless slacker who's been living the life of giving up the spotlight to Kazuya, despite the fact that he may be more gifted than him. Minami is the beautiful childhood girlfriend and for all intents, sister from next door who treats both of them as equals. Society largely assumes Kazuya and Minami will become the perfect couple, including Tatsuya. Yet as time progresses, Tatsuya grows to realize that he's willing to sacrifice anything for the sake of his brother, except at the expense of giving up Minami to Kazuya. And thus the story is told of Tatsuya trying to prove himself over his established younger brother, how it affects the relationship between the three, and both brothers' attempts to make Minami's lifelong dreams come true.

In an alternate 21st century, the robotics industry undergoes a period of rapid advancement worldwide. By the year 2050, Japan has firmly established itself as the leader in robotic technology and manufacture with Daiwa Heavy Industries. As the technology evolves to include robotic enhancements to the human body, the blurring of the line between man and machine triggers a sudden shift in world opinion. In response, the U.N. passes a unilateral ban of further research and development on robotics in 2067. Japan fiercely objects to this ban, but is unable to prevent its passage. In protest, Japan withdrew from international politics and chose to pursue a policy of high-tech national isolation. While only trade continues, Japan disappears from the world scene. Ten years later, a series of bizarre incidents lead the American technology police agency SWORD to believe that Japan has concealed extensive development of banned technologies through the use of the RACE network. SWORD dispatches a unit of special agents to infiltrate Japan and gather intelligence on the country. Vexille, a veteran agent among the group, uncovers the horrifying truth behind the ten years of isolation.

Futuristic post-war Japan is divided into four military regions, each led by conflicting nations trying to gain complete control over the country. While the Boundary War—fought with the help of humanoid mecha weapons called AMAIM—has long been over, the rivalry between these factions is still ongoing, and, as a result, the Japanese are heavily oppressed. Amou Shiiba, a 16-year-old orphan boy who is secretly rebuilding an abandoned AMAIM named Kenbu, stumbles upon Gai, an autonomous AI in need of battery power. By choosing to help one another, Amou and Gai find themselves at the center of a disaster, and Amou is labeled a terrorist and cast out of society. Even so, Amou refuses to remain idle in the face of injustice, and he embarks on a long journey rife with struggle and companionship. His aim transitions from leading a peaceful life to liberating the Japanese people.

The year is 2045, and artificial intelligence has undergone tremendous developments. Governments use them as weapons, engaging in never-ending warfare to sustain their economies. The mercenary group GHOST, headed by Major Motoko Kusanagi, is no stranger to this landscape. However, the rapid innovation of this technology causes a new threat to loom over the horizon. Having left Public Security Section 9, Kusanagi and her group are involved in many operations worldwide related to these proxy wars. But a seemingly simple job of locating an arms dealer drags GHOST into a hidden conflict against cybernetically enhanced individuals, who have inexplicably gained extreme intelligence and physical abilities. Dubbed post-humans, their emergence sets off a chain of events leading to the reunion of Section 9. Armed with a new mission, it is up to Kusanagi and her reestablished team to prevent global chaos at the hands of these post-humans.